The microarray platform selected will have important effects in the later stages, determining the complexity and flexibility of the data to be analyzed. Care must be taken to choose a platform that will allow data to be analyzed and disseminated in the manners desired.

Platform Categories

•  cDNA: Several hundred bases amplified from cDNA
•  Oligo: Oligos synthesized from known sequences
•  One color: One sample, labeled and hybridized to array
•  Two color: Two samples labeled with separate colors and hybridized to one array.

Experimental design and analysis is generally more straightforward with one color microarrays.

Feature extraction

•  Software
•  File Formats
•  CEL, CHP, MAS 5, RMA, etc.
•  GenePix, ImaGene

Data formats will affect the accessibility of the data for analysis, as well as the signal intensities and quality measures available for downstream analysis.